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Make samplesheet #661

Merged
merged 3 commits into from
Jun 18, 2021
Merged

Make samplesheet #661

merged 3 commits into from
Jun 18, 2021

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grst
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@grst grst commented Jun 18, 2021

While creating this PR, I figured it's not that easy after all to use patterns instead of an extension (it breaks the sample name sanitation).
However, I cleaned up a bit and fixed another potential issue when merging replicates:

Globs do not yield sorted results, so it could have happened that e.g. R1 from replicate 1 is matched with R2 from replicate 2 in the samplesheet.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@grst grst requested a review from drpatelh June 18, 2021 11:54
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github-actions bot commented Jun 18, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7164915

+| ✅ 114 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  78 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: environment.yml
  • files_exist - File not found: Dockerfile
  • nextflow_config - Config variable not found: process.container
  • nextflow_config - Config manifest.version should end in dev: '3.2'
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.genome
  • params_used - Config variable not found in main.nf: params.transcript_fasta
  • params_used - Config variable not found in main.nf: params.additional_fasta
  • params_used - Config variable not found in main.nf: params.splicesites
  • params_used - Config variable not found in main.nf: params.gtf_extra_attributes
  • params_used - Config variable not found in main.nf: params.gtf_group_features
  • params_used - Config variable not found in main.nf: params.featurecounts_feature_type
  • params_used - Config variable not found in main.nf: params.featurecounts_group_type
  • params_used - Config variable not found in main.nf: params.gencode
  • params_used - Config variable not found in main.nf: params.save_reference
  • params_used - Config variable not found in main.nf: params.with_umi
  • params_used - Config variable not found in main.nf: params.umitools_extract_method
  • params_used - Config variable not found in main.nf: params.umitools_bc_pattern
  • params_used - Config variable not found in main.nf: params.save_umi_intermeds
  • params_used - Config variable not found in main.nf: params.clip_r1
  • params_used - Config variable not found in main.nf: params.clip_r2
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r1
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r2
  • params_used - Config variable not found in main.nf: params.trim_nextseq
  • params_used - Config variable not found in main.nf: params.save_trimmed
  • params_used - Config variable not found in main.nf: params.skip_trimming
  • params_used - Config variable not found in main.nf: params.remove_ribo_rna
  • params_used - Config variable not found in main.nf: params.save_non_ribo_reads
  • params_used - Config variable not found in main.nf: params.ribo_database_manifest
  • params_used - Config variable not found in main.nf: params.aligner
  • params_used - Config variable not found in main.nf: params.pseudo_aligner
  • params_used - Config variable not found in main.nf: params.seq_center
  • params_used - Config variable not found in main.nf: params.bam_csi_index
  • params_used - Config variable not found in main.nf: params.star_ignore_sjdbgtf
  • params_used - Config variable not found in main.nf: params.salmon_quant_libtype
  • params_used - Config variable not found in main.nf: params.hisat2_build_memory
  • params_used - Config variable not found in main.nf: params.stringtie_ignore_gtf
  • params_used - Config variable not found in main.nf: params.min_mapped_reads
  • params_used - Config variable not found in main.nf: params.save_merged_fastq
  • params_used - Config variable not found in main.nf: params.save_unaligned
  • params_used - Config variable not found in main.nf: params.save_align_intermeds
  • params_used - Config variable not found in main.nf: params.skip_markduplicates
  • params_used - Config variable not found in main.nf: params.skip_alignment
  • params_used - Config variable not found in main.nf: params.skip_qc
  • params_used - Config variable not found in main.nf: params.skip_bigwig
  • params_used - Config variable not found in main.nf: params.skip_stringtie
  • params_used - Config variable not found in main.nf: params.skip_fastqc
  • params_used - Config variable not found in main.nf: params.skip_preseq
  • params_used - Config variable not found in main.nf: params.skip_dupradar
  • params_used - Config variable not found in main.nf: params.skip_qualimap
  • params_used - Config variable not found in main.nf: params.skip_rseqc
  • params_used - Config variable not found in main.nf: params.skip_biotype_qc
  • params_used - Config variable not found in main.nf: params.skip_deseq2_qc
  • params_used - Config variable not found in main.nf: params.skip_multiqc
  • params_used - Config variable not found in main.nf: params.deseq2_vst
  • params_used - Config variable not found in main.nf: params.rseqc_modules
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • params_used - Config variable not found in main.nf: params.multiqc_config
  • params_used - Config variable not found in main.nf: params.multiqc_title
  • params_used - Config variable not found in main.nf: params.email
  • params_used - Config variable not found in main.nf: params.email_on_fail
  • params_used - Config variable not found in main.nf: params.max_multiqc_email_size
  • params_used - Config variable not found in main.nf: params.plaintext_email
  • params_used - Config variable not found in main.nf: params.monochrome_logs
  • params_used - Config variable not found in main.nf: params.help
  • params_used - Config variable not found in main.nf: params.tracedir
  • params_used - Config variable not found in main.nf: params.validate_params
  • params_used - Config variable not found in main.nf: params.enable_conda
  • params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
  • params_used - Config variable not found in main.nf: params.hostnames
  • params_used - Config variable not found in main.nf: params.config_profile_description
  • params_used - Config variable not found in main.nf: params.config_profile_contact
  • params_used - Config variable not found in main.nf: params.config_profile_url
  • params_used - Config variable not found in main.nf: params.max_memory
  • params_used - Config variable not found in main.nf: params.max_cpus
  • params_used - Config variable not found in main.nf: params.max_time
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-18 11:54:28

drpatelh
drpatelh approved these changes Jun 18, 2021
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Looks great! Thank you.

@drpatelh drpatelh merged commit 05e0763 into nf-core:dev Jun 18, 2021
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Tested locally and works like a charm

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@grst @drpatelh